Correlation between copy number variations of arm-level result and selected clinical features

Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1WW7GDX

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 69 arm-level events and 11 clinical features across 198 patients, 47 significant findings detected with Q value < 0.25.

1p gain cnv correlated to 'Time to Death'.
1q gain cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
7q gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.
17p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.M.STAGE'.
3p loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
3q loss cnv correlated to 'Time to Death'.
4p loss cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'GENDER'.
4q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
5p loss cnv correlated to 'Time to Death'.
5q loss cnv correlated to 'Time to Death'.
8q loss cnv correlated to 'Time to Death'.
9p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
9q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
11p loss cnv correlated to 'Time to Death'.
11q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
13q loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'GENDER'.
15q loss cnv correlated to 'Time to Death'.
16q loss cnv correlated to 'Time to Death'.
17p loss cnv correlated to 'Time to Death' and 'NEOPLASM.DISEASESTAGE'.
18p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
18q loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
19p loss cnv correlated to 'Time to Death'.
19q loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
22q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
xq loss cnv correlated to 'Time to Death' and 'PATHOLOGY.T.STAGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 69 arm-level events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 47 significant findings detected.


		Clinical Features	Time to Death	AGE	NEOPLASM DISEASESTAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	PATHOLOGY M STAGE	GENDER	KARNOFSKY PERFORMANCE SCORE	NUMBERPACKYEARSSMOKED	RACE	ETHNICITY
	nCNV (%)	nWild-Type	logrank test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Wilcoxon-test	Wilcoxon-test	Fisher's exact test	Fisher's exact test
13q loss	20 (10%)	178	0.000105 (0.0683)	0.0145 (1.00)	0.0002 (0.129)	0.00013 (0.0846)	0.00591 (1.00)	0.584 (1.00)	8.34e-05 (0.0546)	0.469 (1.00)		0.102 (1.00)	1 (1.00)
1q gain	15 (8%)	183	6.77e-08 (4.62e-05)	0.935 (1.00)	1e-05 (0.00677)	1e-05 (0.00677)	0.184 (1.00)	0.166 (1.00)	0.0419 (1.00)	0.241 (1.00)		0.285 (1.00)	1 (1.00)
3p loss	15 (8%)	183	1.11e-05 (0.00739)	0.171 (1.00)	5e-05 (0.0328)	0.00033 (0.212)	0.884 (1.00)	0.106 (1.00)	0.77 (1.00)	0.317 (1.00)	0.785 (1.00)	0.451 (1.00)	1 (1.00)
4p loss	19 (10%)	179	0.0188 (1.00)	0.00357 (1.00)	1e-05 (0.00677)	1e-05 (0.00677)	0.00255 (1.00)	0.695 (1.00)	3.24e-05 (0.0213)	0.219 (1.00)		0.0962 (1.00)	0.566 (1.00)
18q loss	33 (17%)	165	8.33e-07 (0.000568)	0.462 (1.00)	2e-05 (0.0133)	3e-05 (0.0199)	0.0156 (1.00)	0.0411 (1.00)	0.0926 (1.00)	0.362 (1.00)	0.35 (1.00)	0.258 (1.00)	1 (1.00)
19q loss	12 (6%)	186	4.13e-12 (2.83e-09)	0.839 (1.00)	0.00019 (0.123)	0.00032 (0.206)	0.0793 (1.00)	0.0593 (1.00)	0.114 (1.00)	0.152 (1.00)	0.792 (1.00)	0.826 (1.00)	1 (1.00)
17p gain	120 (61%)	78	0.159 (1.00)	0.0113 (1.00)	3e-05 (0.0199)	0.00059 (0.375)	0.191 (1.00)	0.00024 (0.155)	0.0562 (1.00)	0.954 (1.00)	0.839 (1.00)	0.227 (1.00)	0.277 (1.00)
4q loss	20 (10%)	178	0.0259 (1.00)	0.0322 (1.00)	4e-05 (0.0263)	3e-05 (0.0199)	0.0173 (1.00)	0.264 (1.00)	0.000517 (0.33)	0.152 (1.00)		0.104 (1.00)	0.593 (1.00)
9p loss	25 (13%)	173	0.0115 (1.00)	0.636 (1.00)	1e-05 (0.00677)	1e-05 (0.00677)	0.0584 (1.00)	0.0912 (1.00)	0.00376 (1.00)	0.0166 (1.00)	0.0283 (1.00)	0.0311 (1.00)	0.606 (1.00)
9q loss	26 (13%)	172	0.00566 (1.00)	0.563 (1.00)	3e-05 (0.0199)	1e-05 (0.00677)	0.0468 (1.00)	0.488 (1.00)	0.00514 (1.00)	0.0362 (1.00)	0.148 (1.00)	0.0638 (1.00)	0.603 (1.00)
11q loss	15 (8%)	183	0.0076 (1.00)	0.319 (1.00)	2e-05 (0.0133)	3e-05 (0.0199)	0.0357 (1.00)	0.191 (1.00)	0.38 (1.00)	0.317 (1.00)		0.483 (1.00)	1 (1.00)
17p loss	9 (5%)	189	6.34e-11 (4.34e-08)	0.771 (1.00)	0.00019 (0.123)	0.00103 (0.649)	0.00486 (1.00)	0.0408 (1.00)	0.0199 (1.00)	0.748 (1.00)		1 (1.00)	1 (1.00)
18p loss	32 (16%)	166	0.0014 (0.875)	0.188 (1.00)	3e-05 (0.0199)	1e-05 (0.00677)	0.0598 (1.00)	0.0303 (1.00)	0.0208 (1.00)	0.482 (1.00)	0.511 (1.00)	0.306 (1.00)	1 (1.00)
22q loss	47 (24%)	151	0.00277 (1.00)	0.233 (1.00)	1e-05 (0.00677)	1e-05 (0.00677)	0.0242 (1.00)	0.0389 (1.00)	0.00154 (0.966)	0.496 (1.00)	0.463 (1.00)	0.136 (1.00)	0.407 (1.00)
xq loss	20 (10%)	178	5.9e-06 (0.00401)	0.0901 (1.00)	0.00068 (0.431)	0.00024 (0.155)	0.0233 (1.00)	0.285 (1.00)	0.0398 (1.00)	0.322 (1.00)		0.0979 (1.00)	1 (1.00)
1p gain	6 (3%)	192	1.25e-11 (8.59e-09)	0.718 (1.00)	0.00168 (1.00)	0.00712 (1.00)	0.0444 (1.00)	0.129 (1.00)	0.062 (1.00)			0.43 (1.00)	1 (1.00)
7q gain	121 (61%)	77	0.411 (1.00)	0.128 (1.00)	0.00024 (0.155)	0.00845 (1.00)	0.458 (1.00)	0.632 (1.00)	0.109 (1.00)	0.086 (1.00)	0.885 (1.00)	0.795 (1.00)	0.293 (1.00)
3q loss	4 (2%)	194	8.02e-14 (5.51e-11)	0.123 (1.00)	0.00457 (1.00)	0.00892 (1.00)	0.164 (1.00)	0.199 (1.00)	0.582 (1.00)			1 (1.00)	1 (1.00)
5p loss	7 (4%)	191	6.91e-06 (0.00469)	0.0365 (1.00)	0.014 (1.00)	0.00266 (1.00)	0.0336 (1.00)	0.129 (1.00)	0.0238 (1.00)			1 (1.00)	0.251 (1.00)
5q loss	7 (4%)	191	0.000104 (0.068)	0.00572 (1.00)	0.0224 (1.00)	0.00264 (1.00)	0.046 (1.00)	0.127 (1.00)	0.0238 (1.00)			1 (1.00)	0.251 (1.00)
8q loss	5 (3%)	193	0.000126 (0.0823)	0.997 (1.00)	0.144 (1.00)	0.583 (1.00)		0.251 (1.00)	0.151 (1.00)			0.172 (1.00)	1 (1.00)
11p loss	12 (6%)	186	1.37e-06 (0.000932)	0.0802 (1.00)	0.00631 (1.00)	0.0064 (1.00)	0.0796 (1.00)	0.406 (1.00)	0.339 (1.00)	0.227 (1.00)		0.807 (1.00)	1 (1.00)
15q loss	21 (11%)	177	0.000181 (0.118)	0.0364 (1.00)	0.00118 (0.742)	0.00063 (0.4)	0.058 (1.00)	0.328 (1.00)	0.203 (1.00)	0.227 (1.00)		0.41 (1.00)	1 (1.00)
16q loss	6 (3%)	192	7.46e-07 (0.000509)	0.171 (1.00)	0.022 (1.00)	0.0955 (1.00)	0.166 (1.00)	0.762 (1.00)	0.361 (1.00)			0.629 (1.00)	1 (1.00)
19p loss	13 (7%)	185	0.000385 (0.247)	0.125 (1.00)	0.00799 (1.00)	0.00793 (1.00)	0.0789 (1.00)	0.175 (1.00)	0.53 (1.00)	0.152 (1.00)	0.726 (1.00)	1 (1.00)	1 (1.00)
2p gain	37 (19%)	161	0.869 (1.00)	0.373 (1.00)	0.0613 (1.00)	0.484 (1.00)	0.199 (1.00)	0.00458 (1.00)	0.69 (1.00)	0.886 (1.00)	0.307 (1.00)	0.695 (1.00)	1 (1.00)
2q gain	39 (20%)	159	0.823 (1.00)	0.696 (1.00)	0.0159 (1.00)	0.479 (1.00)	0.104 (1.00)	0.00689 (1.00)	0.559 (1.00)	0.719 (1.00)	0.307 (1.00)	0.623 (1.00)	1 (1.00)
3p gain	58 (29%)	140	0.107 (1.00)	0.796 (1.00)	0.0153 (1.00)	0.0175 (1.00)	0.835 (1.00)	0.21 (1.00)	0.607 (1.00)	0.0208 (1.00)	0.366 (1.00)	0.789 (1.00)	1 (1.00)
3q gain	68 (34%)	130	0.21 (1.00)	0.425 (1.00)	0.0929 (1.00)	0.0972 (1.00)	0.882 (1.00)	0.0853 (1.00)	0.412 (1.00)	0.168 (1.00)	0.549 (1.00)	0.29 (1.00)	0.719 (1.00)
4p gain	6 (3%)	192	0.00876 (1.00)	0.0107 (1.00)	0.0861 (1.00)	0.505 (1.00)	0.468 (1.00)	0.18 (1.00)	0.673 (1.00)			1 (1.00)	1 (1.00)
4q gain	5 (3%)	193	0.00876 (1.00)	0.0336 (1.00)	0.365 (1.00)	0.585 (1.00)	0.148 (1.00)	0.687 (1.00)	1 (1.00)			1 (1.00)	1 (1.00)
5p gain	27 (14%)	171	0.732 (1.00)	0.63 (1.00)	0.322 (1.00)	0.261 (1.00)	0.408 (1.00)	0.428 (1.00)	0.821 (1.00)	0.275 (1.00)	0.693 (1.00)	0.371 (1.00)	0.611 (1.00)
5q gain	27 (14%)	171	0.732 (1.00)	0.971 (1.00)	0.324 (1.00)	0.441 (1.00)	0.77 (1.00)	0.432 (1.00)	0.821 (1.00)	0.275 (1.00)	0.693 (1.00)	0.582 (1.00)	0.361 (1.00)
6p gain	8 (4%)	190	0.603 (1.00)	0.504 (1.00)	0.00289 (1.00)	0.00084 (0.531)	0.258 (1.00)	0.0509 (1.00)	0.695 (1.00)	1 (1.00)		1 (1.00)	1 (1.00)
6q gain	6 (3%)	192	0.859 (1.00)	0.173 (1.00)	0.0148 (1.00)	0.00726 (1.00)	0.0765 (1.00)	0.0182 (1.00)	0.361 (1.00)	1 (1.00)		0.727 (1.00)	1 (1.00)
7p gain	120 (61%)	78	0.426 (1.00)	0.166 (1.00)	0.00046 (0.294)	0.0131 (1.00)	0.586 (1.00)	0.548 (1.00)	0.112 (1.00)	0.086 (1.00)	0.885 (1.00)	0.762 (1.00)	0.299 (1.00)
8p gain	12 (6%)	186	0.0931 (1.00)	0.964 (1.00)	0.169 (1.00)	0.1 (1.00)	0.208 (1.00)	1 (1.00)	0.339 (1.00)			0.118 (1.00)	1 (1.00)
8q gain	17 (9%)	181	0.0931 (1.00)	0.501 (1.00)	0.00194 (1.00)	0.00071 (0.449)	0.0157 (1.00)	0.141 (1.00)	0.0467 (1.00)	0.603 (1.00)		0.0905 (1.00)	1 (1.00)
9p gain	3 (2%)	195		0.477 (1.00)	0.0337 (1.00)	0.0545 (1.00)		0.643 (1.00)	1 (1.00)			0.604 (1.00)	1 (1.00)
10p gain	8 (4%)	190	0.727 (1.00)	0.381 (1.00)	0.215 (1.00)	0.413 (1.00)	1 (1.00)	0.0365 (1.00)	0.695 (1.00)			0.00498 (1.00)	1 (1.00)
10q gain	8 (4%)	190	0.727 (1.00)	0.381 (1.00)	0.217 (1.00)	0.411 (1.00)	1 (1.00)	0.037 (1.00)	0.695 (1.00)			0.0045 (1.00)	1 (1.00)
11p gain	10 (5%)	188	0.603 (1.00)	0.217 (1.00)	0.0452 (1.00)	0.0303 (1.00)	0.558 (1.00)	0.0473 (1.00)	0.161 (1.00)			0.337 (1.00)	1 (1.00)
11q gain	9 (5%)	189	0.603 (1.00)	0.0943 (1.00)	0.134 (1.00)	0.0615 (1.00)	0.723 (1.00)	0.263 (1.00)	0.0199 (1.00)			0.349 (1.00)	1 (1.00)
12p gain	81 (41%)	117	0.0904 (1.00)	0.328 (1.00)	0.158 (1.00)	0.474 (1.00)	0.623 (1.00)	0.203 (1.00)	0.0171 (1.00)	0.356 (1.00)	0.541 (1.00)	0.63 (1.00)	0.0796 (1.00)
12q gain	81 (41%)	117	0.0904 (1.00)	0.328 (1.00)	0.161 (1.00)	0.476 (1.00)	0.627 (1.00)	0.2 (1.00)	0.0171 (1.00)	0.356 (1.00)	0.541 (1.00)	0.631 (1.00)	0.0796 (1.00)
13q gain	22 (11%)	176	0.875 (1.00)	0.459 (1.00)	0.568 (1.00)	0.553 (1.00)	0.725 (1.00)	0.855 (1.00)	1 (1.00)	0.318 (1.00)		0.734 (1.00)	0.285 (1.00)
14q gain	3 (2%)	195			0.0553 (1.00)	0.0223 (1.00)		0.643 (1.00)	0.206 (1.00)				1 (1.00)
15q gain	5 (3%)	193	0.597 (1.00)	0.891 (1.00)	0.182 (1.00)	0.245 (1.00)		0.503 (1.00)	0.151 (1.00)			0.677 (1.00)	1 (1.00)
16p gain	106 (54%)	92	0.18 (1.00)	0.156 (1.00)	0.821 (1.00)	0.659 (1.00)	1 (1.00)	0.562 (1.00)	0.00507 (1.00)	0.679 (1.00)	0.383 (1.00)	0.036 (1.00)	0.0824 (1.00)
16q gain	102 (52%)	96	0.0406 (1.00)	0.334 (1.00)	0.472 (1.00)	0.3 (1.00)	0.768 (1.00)	0.151 (1.00)	0.0419 (1.00)	0.233 (1.00)	0.794 (1.00)	0.161 (1.00)	0.0896 (1.00)
17q gain	135 (68%)	63	0.263 (1.00)	0.0514 (1.00)	0.0465 (1.00)	0.205 (1.00)	0.369 (1.00)	0.00229 (1.00)	0.406 (1.00)	0.76 (1.00)	0.503 (1.00)	0.416 (1.00)	0.265 (1.00)
18p gain	9 (5%)	189	0.201 (1.00)	0.925 (1.00)	0.368 (1.00)	1 (1.00)	0.64 (1.00)	0.121 (1.00)	0.288 (1.00)	0.623 (1.00)		0.32 (1.00)	1 (1.00)
18q gain	6 (3%)	192	0.623 (1.00)	0.797 (1.00)	0.621 (1.00)	0.634 (1.00)		0.344 (1.00)	0.673 (1.00)	0.0964 (1.00)		0.336 (1.00)	1 (1.00)
19p gain	4 (2%)	194	0.779 (1.00)	0.0504 (1.00)	0.573 (1.00)	0.527 (1.00)	1 (1.00)	0.442 (1.00)	0.582 (1.00)			0.0944 (1.00)	1 (1.00)
19q gain	4 (2%)	194	0.779 (1.00)	0.0504 (1.00)	0.57 (1.00)	0.528 (1.00)	1 (1.00)	0.442 (1.00)	0.582 (1.00)			0.0948 (1.00)	1 (1.00)
20p gain	69 (35%)	129	0.897 (1.00)	0.25 (1.00)	0.377 (1.00)	0.4 (1.00)	1 (1.00)	0.896 (1.00)	0.624 (1.00)	0.389 (1.00)	0.588 (1.00)	0.689 (1.00)	0.495 (1.00)
20q gain	71 (36%)	127	0.919 (1.00)	0.232 (1.00)	0.214 (1.00)	0.286 (1.00)	0.902 (1.00)	0.836 (1.00)	0.516 (1.00)	0.389 (1.00)	0.588 (1.00)	0.601 (1.00)	0.492 (1.00)
21q gain	12 (6%)	186	0.677 (1.00)	0.135 (1.00)	0.858 (1.00)	1 (1.00)	0.637 (1.00)	0.125 (1.00)	0.75 (1.00)	0.931 (1.00)		0.0494 (1.00)	0.478 (1.00)
xq gain	67 (34%)	131	0.287 (1.00)	0.71 (1.00)	0.00613 (1.00)	0.0184 (1.00)	0.572 (1.00)	0.679 (1.00)	0.0709 (1.00)	0.0448 (1.00)	0.746 (1.00)	0.311 (1.00)	0.72 (1.00)
1p loss	20 (10%)	178	0.115 (1.00)	0.313 (1.00)	0.0843 (1.00)	0.0853 (1.00)	0.308 (1.00)	0.769 (1.00)	0.122 (1.00)	0.806 (1.00)		0.448 (1.00)	0.593 (1.00)
1q loss	13 (7%)	185	0.6 (1.00)	0.265 (1.00)	0.288 (1.00)	0.603 (1.00)	0.724 (1.00)	0.473 (1.00)	0.208 (1.00)	0.812 (1.00)		0.401 (1.00)	0.538 (1.00)
6p loss	15 (8%)	183	0.147 (1.00)	0.328 (1.00)	0.0236 (1.00)	0.0405 (1.00)	0.0508 (1.00)	0.611 (1.00)	0.144 (1.00)	0.753 (1.00)		0.0438 (1.00)	1 (1.00)
6q loss	18 (9%)	180	0.697 (1.00)	0.836 (1.00)	0.0358 (1.00)	0.00166 (1.00)	0.117 (1.00)	0.303 (1.00)	0.0148 (1.00)	0.469 (1.00)	0.392 (1.00)	0.0214 (1.00)	1 (1.00)
8p loss	10 (5%)	188	0.000536 (0.342)	0.303 (1.00)	0.0281 (1.00)	0.438 (1.00)	0.00672 (1.00)	0.00806 (1.00)	0.161 (1.00)	0.748 (1.00)		0.019 (1.00)	1 (1.00)
10p loss	12 (6%)	186	0.00691 (1.00)	0.994 (1.00)	0.00125 (0.785)	0.00365 (1.00)	0.0685 (1.00)	0.0386 (1.00)	0.114 (1.00)	0.241 (1.00)		0.826 (1.00)	1 (1.00)
10q loss	12 (6%)	186	0.0041 (1.00)	0.373 (1.00)	0.00058 (0.369)	0.00089 (0.562)	0.0282 (1.00)	0.126 (1.00)	0.114 (1.00)	0.0757 (1.00)		0.398 (1.00)	1 (1.00)
14q loss	36 (18%)	162	0.00312 (1.00)	0.832 (1.00)	0.00249 (1.00)	0.00207 (1.00)	0.0455 (1.00)	0.135 (1.00)	0.0042 (1.00)	0.0943 (1.00)	0.213 (1.00)	0.953 (1.00)	1 (1.00)
16p loss	4 (2%)	194		0.672 (1.00)	0.133 (1.00)	0.0934 (1.00)		1 (1.00)	0.0764 (1.00)				1 (1.00)
21q loss	32 (16%)	166	0.295 (1.00)	0.503 (1.00)	0.00882 (1.00)	0.00467 (1.00)	0.646 (1.00)	0.21 (1.00)	0.058 (1.00)	0.105 (1.00)	0.456 (1.00)	0.482 (1.00)	1 (1.00)

'1p gain' versus 'Time to Death'

P value = 1.25e-11 (logrank test), Q value = 8.6e-09

Table S1. Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
1P GAIN MUTATED	4	1	26.0 - 112.0 (74.5)
1P GAIN WILD-TYPE	169	6	2.0 - 5925.0 (511.0)

Figure S1. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'Time to Death'

P value = 6.77e-08 (logrank test), Q value = 4.6e-05

Table S2. Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
1Q GAIN MUTATED	12	3	21.0 - 1967.0 (99.5)
1Q GAIN WILD-TYPE	161	4	2.0 - 5925.0 (516.0)

Figure S2. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S3. Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
1Q GAIN MUTATED	1	0	11	3
1Q GAIN WILD-TYPE	121	11	31	9

Figure S3. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'1q gain' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S4. Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
1Q GAIN MUTATED	2	0	13
1Q GAIN WILD-TYPE	128	18	37

Figure S4. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'7q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S5. Gene #14: '7q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
7Q GAIN MUTATED	86	4	15	8
7Q GAIN WILD-TYPE	36	7	27	4

Figure S5. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'17p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S6. Gene #29: '17p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
17P GAIN MUTATED	88	6	15	3
17P GAIN WILD-TYPE	34	5	27	9

Figure S6. Get High-res Image Gene #29: '17p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'17p gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S7. Gene #29: '17p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1	MX
ALL	81	8	96
17P GAIN MUTATED	38	2	70
17P GAIN WILD-TYPE	43	6	26

Figure S7. Get High-res Image Gene #29: '17p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'3p loss' versus 'Time to Death'

P value = 1.11e-05 (logrank test), Q value = 0.0074

Table S8. Gene #41: '3p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
3P LOSS MUTATED	13	3	4.0 - 2429.0 (112.0)
3P LOSS WILD-TYPE	160	4	2.0 - 5925.0 (542.0)

Figure S8. Get High-res Image Gene #41: '3p loss' versus Clinical Feature #1: 'Time to Death'

'3p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S9. Gene #41: '3p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
3P LOSS MUTATED	2	1	9	3
3P LOSS WILD-TYPE	120	10	33	9

Figure S9. Get High-res Image Gene #41: '3p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'3p loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.00033 (Fisher's exact test), Q value = 0.21

Table S10. Gene #41: '3p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
3P LOSS MUTATED	3	2	10
3P LOSS WILD-TYPE	127	16	40

Figure S10. Get High-res Image Gene #41: '3p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'3q loss' versus 'Time to Death'

P value = 8.02e-14 (logrank test), Q value = 5.5e-11

Table S11. Gene #42: '3q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
3Q LOSS MUTATED	3	2	112.0 - 270.0 (208.0)
3Q LOSS WILD-TYPE	170	5	2.0 - 5925.0 (510.5)

Figure S11. Get High-res Image Gene #42: '3q loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S12. Gene #43: '4p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
4P LOSS MUTATED	3	1	14	1
4P LOSS WILD-TYPE	119	10	28	11

Figure S12. Get High-res Image Gene #43: '4p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'4p loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S13. Gene #43: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
4P LOSS MUTATED	3	2	14
4P LOSS WILD-TYPE	127	16	36

Figure S13. Get High-res Image Gene #43: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'4p loss' versus 'GENDER'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.021

Table S14. Gene #43: '4p loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	58	140
4P LOSS MUTATED	14	5
4P LOSS WILD-TYPE	44	135

Figure S14. Get High-res Image Gene #43: '4p loss' versus Clinical Feature #7: 'GENDER'

'4q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S15. Gene #44: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
4Q LOSS MUTATED	4	1	13	2
4Q LOSS WILD-TYPE	118	10	29	10

Figure S15. Get High-res Image Gene #44: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'4q loss' versus 'PATHOLOGY.T.STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S16. Gene #44: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
4Q LOSS MUTATED	4	3	13
4Q LOSS WILD-TYPE	126	15	37

Figure S16. Get High-res Image Gene #44: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'5p loss' versus 'Time to Death'

P value = 6.91e-06 (logrank test), Q value = 0.0047

Table S17. Gene #45: '5p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
5P LOSS MUTATED	4	1	21.0 - 554.0 (90.5)
5P LOSS WILD-TYPE	169	6	2.0 - 5925.0 (510.0)

Figure S17. Get High-res Image Gene #45: '5p loss' versus Clinical Feature #1: 'Time to Death'

'5q loss' versus 'Time to Death'

P value = 0.000104 (logrank test), Q value = 0.068

Table S18. Gene #46: '5q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
5Q LOSS MUTATED	5	1	21.0 - 554.0 (97.0)
5Q LOSS WILD-TYPE	168	6	2.0 - 5925.0 (510.5)

Figure S18. Get High-res Image Gene #46: '5q loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'Time to Death'

P value = 0.000126 (logrank test), Q value = 0.082

Table S19. Gene #50: '8q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
8Q LOSS MUTATED	4	1	10.0 - 307.0 (155.0)
8Q LOSS WILD-TYPE	169	6	2.0 - 5925.0 (511.0)

Figure S19. Get High-res Image Gene #50: '8q loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S20. Gene #51: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
9P LOSS MUTATED	5	0	13	5
9P LOSS WILD-TYPE	117	11	29	7

Figure S20. Get High-res Image Gene #51: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9p loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S21. Gene #51: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
9P LOSS MUTATED	6	2	17
9P LOSS WILD-TYPE	124	16	33

Figure S21. Get High-res Image Gene #51: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S22. Gene #52: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
9Q LOSS MUTATED	6	1	14	4
9Q LOSS WILD-TYPE	116	10	28	8

Figure S22. Get High-res Image Gene #52: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9q loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S23. Gene #52: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
9Q LOSS MUTATED	7	1	18
9Q LOSS WILD-TYPE	123	17	32

Figure S23. Get High-res Image Gene #52: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'11p loss' versus 'Time to Death'

P value = 1.37e-06 (logrank test), Q value = 0.00093

Table S24. Gene #55: '11p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
11P LOSS MUTATED	10	3	21.0 - 1967.0 (246.5)
11P LOSS WILD-TYPE	163	4	2.0 - 5925.0 (510.0)

Figure S24. Get High-res Image Gene #55: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S25. Gene #56: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
11Q LOSS MUTATED	2	1	8	4
11Q LOSS WILD-TYPE	120	10	34	8

Figure S25. Get High-res Image Gene #56: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'11q loss' versus 'PATHOLOGY.T.STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S26. Gene #56: '11q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
11Q LOSS MUTATED	2	1	12
11Q LOSS WILD-TYPE	128	17	38

Figure S26. Get High-res Image Gene #56: '11q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'13q loss' versus 'Time to Death'

P value = 0.000105 (logrank test), Q value = 0.068

Table S27. Gene #57: '13q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
13Q LOSS MUTATED	16	3	4.0 - 2639.0 (84.5)
13Q LOSS WILD-TYPE	157	4	2.0 - 5925.0 (543.0)

Figure S27. Get High-res Image Gene #57: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.13

Table S28. Gene #57: '13q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
13Q LOSS MUTATED	5	1	11	3
13Q LOSS WILD-TYPE	117	10	31	9

Figure S28. Get High-res Image Gene #57: '13q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'13q loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.085

Table S29. Gene #57: '13q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
13Q LOSS MUTATED	5	2	13
13Q LOSS WILD-TYPE	125	16	37

Figure S29. Get High-res Image Gene #57: '13q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'13q loss' versus 'GENDER'

P value = 8.34e-05 (Fisher's exact test), Q value = 0.055

Table S30. Gene #57: '13q loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	58	140
13Q LOSS MUTATED	14	6
13Q LOSS WILD-TYPE	44	134

Figure S30. Get High-res Image Gene #57: '13q loss' versus Clinical Feature #7: 'GENDER'

'15q loss' versus 'Time to Death'

P value = 0.000181 (logrank test), Q value = 0.12

Table S31. Gene #59: '15q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
15Q LOSS MUTATED	16	3	3.0 - 5925.0 (207.5)
15Q LOSS WILD-TYPE	157	4	2.0 - 3950.0 (516.0)

Figure S31. Get High-res Image Gene #59: '15q loss' versus Clinical Feature #1: 'Time to Death'

'16q loss' versus 'Time to Death'

P value = 7.46e-07 (logrank test), Q value = 0.00051

Table S32. Gene #61: '16q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
16Q LOSS MUTATED	3	2	21.0 - 1967.0 (87.0)
16Q LOSS WILD-TYPE	170	5	2.0 - 5925.0 (509.0)

Figure S32. Get High-res Image Gene #61: '16q loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'Time to Death'

P value = 6.34e-11 (logrank test), Q value = 4.3e-08

Table S33. Gene #62: '17p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
17P LOSS MUTATED	4	1	7.0 - 208.0 (39.0)
17P LOSS WILD-TYPE	169	6	2.0 - 5925.0 (511.0)

Figure S33. Get High-res Image Gene #62: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S34. Gene #62: '17p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
17P LOSS MUTATED	1	1	3	4
17P LOSS WILD-TYPE	121	10	39	8

Figure S34. Get High-res Image Gene #62: '17p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S35. Gene #63: '18p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
18P LOSS MUTATED	9	1	15	5
18P LOSS WILD-TYPE	113	10	27	7

Figure S35. Get High-res Image Gene #63: '18p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18p loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S36. Gene #63: '18p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
18P LOSS MUTATED	9	3	20
18P LOSS WILD-TYPE	121	15	30

Figure S36. Get High-res Image Gene #63: '18p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'18q loss' versus 'Time to Death'

P value = 8.33e-07 (logrank test), Q value = 0.00057

Table S37. Gene #64: '18q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
18Q LOSS MUTATED	27	6	4.0 - 3760.0 (232.0)
18Q LOSS WILD-TYPE	146	1	2.0 - 5925.0 (528.5)

Figure S37. Get High-res Image Gene #64: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S38. Gene #64: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
18Q LOSS MUTATED	9	1	16	5
18Q LOSS WILD-TYPE	113	10	26	7

Figure S38. Get High-res Image Gene #64: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18q loss' versus 'PATHOLOGY.T.STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S39. Gene #64: '18q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
18Q LOSS MUTATED	10	3	20
18Q LOSS WILD-TYPE	120	15	30

Figure S39. Get High-res Image Gene #64: '18q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'19p loss' versus 'Time to Death'

P value = 0.000385 (logrank test), Q value = 0.25

Table S40. Gene #65: '19p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
19P LOSS MUTATED	13	3	29.0 - 2584.0 (223.0)
19P LOSS WILD-TYPE	160	4	2.0 - 5925.0 (509.0)

Figure S40. Get High-res Image Gene #65: '19p loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'Time to Death'

P value = 4.13e-12 (logrank test), Q value = 2.8e-09

Table S41. Gene #66: '19q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
19Q LOSS MUTATED	12	4	29.0 - 1967.0 (152.5)
19Q LOSS WILD-TYPE	161	3	2.0 - 5925.0 (511.0)

Figure S41. Get High-res Image Gene #66: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S42. Gene #66: '19q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
19Q LOSS MUTATED	1	1	8	1
19Q LOSS WILD-TYPE	121	10	34	11

Figure S42. Get High-res Image Gene #66: '19q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'19q loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.00032 (Fisher's exact test), Q value = 0.21

Table S43. Gene #66: '19q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
19Q LOSS MUTATED	2	1	9
19Q LOSS WILD-TYPE	128	17	41

Figure S43. Get High-res Image Gene #66: '19q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'22q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S44. Gene #68: '22q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
22Q LOSS MUTATED	14	3	21	7
22Q LOSS WILD-TYPE	108	8	21	5

Figure S44. Get High-res Image Gene #68: '22q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'22q loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0068

Table S45. Gene #68: '22q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
22Q LOSS MUTATED	17	3	27
22Q LOSS WILD-TYPE	113	15	23

Figure S45. Get High-res Image Gene #68: '22q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'xq loss' versus 'Time to Death'

P value = 5.9e-06 (logrank test), Q value = 0.004

Table S46. Gene #69: 'xq loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
XQ LOSS MUTATED	16	4	4.0 - 2429.0 (288.5)
XQ LOSS WILD-TYPE	157	3	2.0 - 5925.0 (541.0)

Figure S46. Get High-res Image Gene #69: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S47. Gene #69: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
XQ LOSS MUTATED	6	1	13
XQ LOSS WILD-TYPE	124	17	37

Figure S47. Get High-res Image Gene #69: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = KIRP-TP.merged_data.txt
Number of patients = 198
Number of significantly arm-level cnvs = 69
Number of selected clinical features = 11
Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

Made with Nozzle